miRNA display CGI

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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
7241	5'	-52.9	NC_001900.1	+	30094	0.67	0.787974
	Target:  5'- gGUCcUCGGAGUCccGAGUguccaggaacgucUGGACCCa -3' miRNA:   3'- -CGGuAGCUUCAGaaCUCA-------------GCCUGGGc -5'
7241	5'	-52.9	NC_001900.1	+	40454	0.68	0.715845
	Target:  5'- aGCCGUCc-AGUCguugGAcUUGGACCCGu -3' miRNA:   3'- -CGGUAGcuUCAGaa--CUcAGCCUGGGC- -5'
7241	5'	-52.9	NC_001900.1	+	48166	0.69	0.682993
	Target:  5'- uGCUGUCGAAGcCauucgcgaaugUUGGGUCGGGCUgCGg -3' miRNA:   3'- -CGGUAGCUUCaG-----------AACUCAGCCUGG-GC- -5'
7241	5'	-52.9	NC_001900.1	+	37465	0.7	0.605103
	Target:  5'- uGCCucGUCGuAGGUCUucgGAGUCGGuuCCa -3' miRNA:   3'- -CGG--UAGC-UUCAGAa--CUCAGCCugGGc -5'
7241	5'	-52.9	NC_001900.1	+	31294	0.71	0.56089
	Target:  5'- cGCCAcCGAAGUUgaucgUGGcguuGUCGGugCCGc -3' miRNA:   3'- -CGGUaGCUUCAGa----ACU----CAGCCugGGC- -5'
7241	5'	-52.9	NC_001900.1	+	43879	0.72	0.496467
	Target:  5'- uGCCAcuUCGGcauGUC-UGGGaUCGGACCCa -3' miRNA:   3'- -CGGU--AGCUu--CAGaACUC-AGCCUGGGc -5'
7241	5'	-52.9	NC_001900.1	+	3162	1.12	0.001177
	Target:  5'- gGCCAUCGAAGUCUUGAGUCGGACCCGa -3' miRNA:   3'- -CGGUAGCUUCAGAACUCAGCCUGGGC- -5'

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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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